Hi,
Taking the two sentences:
“Only you can stop you from running”
and:
‘Only you, can stop you running.’,
how would you comment on the comma\its absence there?
Both sentences should be:
Only you can stop yourself (from) running.
…But unfortunately, they aren’t. Being put that way, does a comma matter at all?
A comma would make the sentence in #2 incorrect also.
I’d agree with Bev. However, if you are bent upon using the comma, then the sentence may change into something like this: Only you, you alone can stop yourself running. (The reflexive is also necessary in place of the subjective pronoun)
To take that one step further, the more natural phrasing would be:
(Only) you, and you alone, can stop yourself running.
(‘Only’ and ‘alone’ are not both needed, though it adds emphasis to use them both.)
Yes, I meant to emphasize.
You, you alone … OR You, only you … . (In either case, if the first comma is placed, I doubt whether ‘and’ and the second comma are necessary)
You and you alone … . OR You and only you … . (I think this can go with the same emphasis and meaning)
And this serves just as an another example of how far apart can be the grammar we’re taught and colloquial speech (English born and bred in both cases). 
“The greatest mistake you can make in life is to be continually fearing you will make one.”
The commas are optional, to denote a larger pause, but if the first is used, I’d argue the second is needed.
The ‘and’ is usual in any instance. It sounds very strange to my UK ears to leave it out.